There is a heater fan switch on the dash. There are two positions; one for high and the other for low. There is also a deflector in the heater itself, make sure it is not sending all your heat right up to the windshield.

My FJ40 gets pretty toasty warm, but it certainly takes a while for the engine to come up to temperature and making good heat.

Yes, the Mule had a soft top and the heater on low would keep it toasty warm. If your blower motor is working (with the engine off, key on and blower motor switch on, open the hood, listen in the engine compartment next to the firewall on the passenger side) then you need to make sure A-The heater box isnt blocked, if it is it wont blow much air. If it is moving a fair amount of air but the air wont get warm even though the engine is at operating temp, then its probably the water control valve. The only other issue would be if your engine isnt warming up because of a bad thermostat.

It is pretty common for the heater boxes to get blocked, either by leaves and such or because the foam parts inside have degraded and fallen apart. If you decide to tear your heater box apart to clean it out, I have a rebuild kit that includes all the proper foam pieces I'll let you have for $20.